package com.utilities.pipelineScripts;

import java.util.ArrayList;

import com.utilities.IO.FileUtilities;
import com.utilities.dataStructures.Range;
import com.utilities.fastaUtilities.MummerUtilities;
import com.utilities.fastaUtilities.OtherUtilities;

public class Test 
{
	public static void main(String[] args) throws Exception
	{
//		String gbkFile = "C:/Users/bansalp/Desktop/data/gbkFile.gbk";
//		String refSeqFile = "C:/Users/bansalp/Desktop/data/referenceSeq.fna";
//		OtherUtilities.fetchReferenceSeq(gbkFile, refSeqFile);
		
		String tilingFile = "C:/Users/bansalp/Desktop/data/tiling.txt";
		String gapsFile = "C:/Users/bansalp/Desktop/data/gaps.txt";
		ArrayList<Range> gaps = MummerUtilities.getGaps(tilingFile);
		FileUtilities.WriteToFile(gaps, gapsFile, 1);
	}
}
